AI Article Synopsis
- Structural variation in cancer affects DNA methylation and gene expression, influencing the molecular makeup of tumors.
- A study analyzed over 2400 pediatric brain and CNS tumors, revealing hundreds of genes linked to structural variant breakpoints that affect methylation and expression, including key tumor suppressors like ATRX and CDKN2A.
- Changes in DNA methylation are not only associated with tumor progression but can also predict patient survival, highlighting important genetic mechanisms across various tumor types.
Article Abstract
Structural variation heavily influences the molecular landscape of cancer, in part by impacting DNA methylation-mediated transcriptional regulation. Here, using multi-omic datasets involving >2400 pediatric brain and central nervous system tumors of diverse histologies from the Children's Brain Tumor Network, we report hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of somatic structural variant (SV) breakpoints is recurrently associated with altered expression or DNA methylation, respectively, including tumor suppressor genes ATRX and CDKN2A. Altered DNA methylation near enhancers associates with nearby somatic SV breakpoints, including MYC and MYCN. A subset of genes with SV-CGI methylation associations also have expression associations with patient survival, including BCOR, TERT, RCOR2, and PDLIM4. DNA methylation changes in recurrent or progressive tumors compared to the initial tumor within the same patient can predict survival in pediatric and adult cancers. Our comprehensive and pan-histology genomic analyses reveal mechanisms of noncoding alterations impacting cancer genes.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310301 | PMC |
| http://dx.doi.org/10.1038/s41467-024-51276-y | DOI Listing |
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